The mouse t-complex on chromosome 17 has long been a focus of interest for developmental biologists. Because many embryonic lethal mutations are localized in the region, and corresponding genes of importance in development are therefore inferred to reside there, it is a prime target for high priority sequence analysis. The findings of our collaborators that the region contains a large number of otherwise unknown genes, including many expressed selectively in the ectoplacental cone, both underlines the importance of the region and provides probes to screen for substrates for long-range sequence analysis. We have thus started to analyze a multimegabase portion of the t- complex. From the initially targeted 1 Mb of overlapping bacterial artificial chromosomes, the sequencing of one 175 kb clone has been completed with greater than 99.9% accuracy. Because very little mouse genomic sequence is available, the analysis must bootstrap from several starting sources. The analysis is therefore incomplete, but the results are encouraging. Our main tools for the analysis are the GENBANK EST database, the exon- predicting program GRAIL, the repetitive sequence finding program CENSOR, and the use of CpG content as an assay for CpG islands and genes. Thus far, four genes have been identified and verified, including the nown gene for ALS 9 which binds and stabilizes the IGF/IGFBP3 complex in serum), the round sperm gene (RSP29), and two newly discovered genes, one of which shows significant sequence to a human nucleotide-binding protein. CpG islands and other EST hits extend the likely catalogue to up to 11 genes in the DNA. This would yield an average of 1 gene/ 15 kb, making this zone of the t-complex part of the highest gene density fraction (2 to 5%) of the genome.